Larval drift and dispersal are critical processes that affect recruitment success for many riverine fishes. Hypolimnetic discharge from the Three Gorges Dam (TGD) lowers river temperature and reduces downstream nutrients, inducing distinct shifts in habitat conditions downstream of the dam. The inflow of major tributaries buffers these influences and creates physiochemical gradients according to the distance from the dam. We investigated the abundance, feeding, and growth of larvae of four major Chinese carps in three sections of the middle Yangtze River. Water temperature and transparency showed clear spatial gradients. Larvae in the river section closest to the dam tended to be lower in abundance and temporally delayed peak abundance and showed lower feeding intensity, poorer condition, and slower growth than those further from the dam. Our results demonstrate that physiochemical gradients influenced by the TGD have strong effects on abundance, feeding, and growth of the drifting larvae. We recommend that river sections farther from the TGD, particularly around the mouth of Poyang Lake, should become high-priority conservation areas to enhance protection of critical aquatic species.